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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1N7M
Germline 7G12 with N-methylmesoporphyrin
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
4.2
Temperature
277.0
Details
22% PEG2000MME, 0.2M Ammonium Sulfate, 10mM Cd Sulfate, 1mM NMP, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 55.27
α = 90
b = 76.24
β = 93.33
c = 60.44
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
SSRL BEAMLINE BL11-1
--
SSRL
BL11-1
Data Collection
Overall
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
R Sym I (Observed)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
1.8
19.79
--
--
--
--
--
44580
44580
0.0
-3.0
23.8
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
MOLECULAR REPLACEMENT
1.8
19.79
--
2.0
46434
44164
1341
95.1
--
--
0.22
0.253
random
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
1.8
1.88
4049
145
3904
0.315
0.304
0.025
69.9
X Ray Diffraction
1.88
1.98
5426
160
5266
0.247
0.242
0.019
93.6
X Ray Diffraction
1.98
2.1
5681
176
5505
0.228
0.227
0.017
98.2
X Ray Diffraction
2.1
2.27
5733
195
5538
0.226
0.228
0.016
98.9
X Ray Diffraction
2.27
2.49
5769
158
5611
0.228
0.229
0.018
99.5
X Ray Diffraction
2.49
2.86
5796
181
5615
0.226
0.228
0.017
99.8
X Ray Diffraction
2.86
3.59
5812
153
5659
0.226
0.231
0.019
99.9
X Ray Diffraction
3.59
19.79
5898
173
5725
0.198
0.196
0.015
99.9
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
30.79
Anisotropic B[1][1]
1.43
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
4.95
Anisotropic B[2][2]
3.94
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-5.37
RMS Deviations
Key
Refinement Restraint Deviation
x_angle_deg
1.3
x_torsion_deg
26.7
x_torsion_impr_deg
0.78
x_bond_d
0.005
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.22
Luzzati Sigma A (Observed)
0.13
Luzzati Resolution Cutoff (Low)
5.0
Luzzati ESD (R-Free Set)
0.26
Luzzati Sigma A (R-Free Set)
0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
3261
Nucleic Acid Atoms
0
Heterogen Atoms
43
Solvent Atoms
505
Software
Software
Software Name
Purpose
CNS
refinement version: 1.0
DENZO
data reduction
SCALEPACK
data scaling
EPMR
phasing